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OPENSEQ.org
Marin
Genes: A B A+B
Length: 319 377 636
Sequences: 22153 1204 144
Seq/Len: 69.45 3.19 0.23
MirrorTree (Pazo et al. 2001) 0.06
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.18 0.07 0.02
2 0.20 0.07 0.02
5 0.23 0.08 0.03
10 0.25 0.08 0.03
20 0.27 0.09 0.06
100 0.31 0.11 0.14
∞ 0.32 0.13 0.21
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
134_S 150_R 1.11 0.17 0.00
28_I 36_K 0.96 0.12 0.00
222_K 149_I 0.95 0.12 0.00
283_L 181_L 0.94 0.12 0.00
158_S 100_V 0.94 0.12 0.00
113_C 188_D 0.93 0.11 0.00
188_F 298_E 0.92 0.11 0.00
68_V 366_I 0.91 0.11 0.00
136_R 36_K 0.90 0.11 0.00
181_V 255_V 0.89 0.10 0.00
296_R 295_L 0.89 0.10 0.00
122_A 340_K 0.88 0.10 0.00
73_L 188_D 0.87 0.10 0.00
281_C 312_F 0.87 0.10 0.00
193_P 196_I 0.86 0.10 0.00
149_V 26_E 0.85 0.10 0.00
103_V 182_D 0.85 0.10 0.00
70_D 225_G 0.84 0.09 0.00
236_V 368_H 0.83 0.09 0.00
195_G 165_R 0.82 0.09 0.00
123_I 47_R 0.82 0.09 0.00
241_P 349_A 0.81 0.09 0.00
62_Y 89_Y 0.81 0.09 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
13473 0.23 Marin Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13472 0.07 Marin Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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